Halliday & Matthiessen (2014: 530):
Traditional school exercises of the kind ‘turn into direct/indirect speech’ suggest that the two always fully match. This is true lexicogrammatically, in that it is always possible to find an equivalent – although not always a unique one: given Mary said she had seen it, the quoted equivalent might be I have seen it, I had seen it or I saw it, or she (someone else) has seen it, etc. But it is not true as a general statement about usage. Semantically the two do not exactly match, and there are many instances where it does not make sense to replace one by the other. Note, for example, Alice thought that that was the jury-box, where we should have to change Alice thought to something like Alice said to herself in order to avoid the sense of ‘held the opinion’, which is the natural interpretation of a verb of thinking when it is projecting by hypotaxis.